Autoexec.bat to cdrw

Hello All,
I have never come across this before but i have to say my knowledge of burning cds is fairly basic. I am trying to copy files to cd including an autoexec.bat file but when i check the disk the autoexec.bat file is missing every time. I am using Nero Burning Rom 6. What i am trying to do is write microcode i.e. upgrade the firmware of my hard disk to correct an annoying clicking noise with my Hitachi Travelstar HD. So i will be booting the laptop from the CD which i assume is presently failing as the above file is missing. Can someone pls tell me where i am going wrong.
Any Help would be appreciated
Fergus

Ah just realised that there is a setting "Hide protected operating system files" in explorer which is unrelated to the setting "Show hidden files and folders" which i had ticked but had forgotten about the former setting.